Showing papers on "Virus classification published in 2010"

Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

Abstract: Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species. In addition, the viruses could also benefit, as some resistant species (e.g. bats) may serve as natural reservoirs for their persistence and transmission. Given the stringent limitations imposed in this informatics search, the examples described here should be considered a low estimate of the number of such integration events that have persisted over evolutionary time scales. Clearly, the sources of genetic information in vertebrate genomes are much more diverse than previously suspected.

Orthopoxvirus genome evolution: the role of gene loss.

Abstract: Poxviruses are highly successful pathogens, known to infect a variety of hosts The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets These techniques allowed us to unambiguously identify the gene loss/gain events that have occurred over the course of orthopoxvirus evolution It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche

Defining Life: The Virus Viewpoint

Abstract: Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors. I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition.

Why genes overlap in viruses

Abstract: The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old

Abstract: Vertebrate genomic assemblies were analyzed for endogenous sequences related to any known viruses with single-stranded DNA genomes. Numerous high-confidence examples related to the Circoviridae and two genera in the family Parvoviridae, the parvoviruses and dependoviruses, were found and were broadly distributed among 31 of the 49 vertebrate species tested. Our analyses indicate that the ages of both virus families may exceed 40 to 50 million years. Shared features of the replication strategies of these viruses may explain the high incidence of the integrations.

Order to the viral universe

Abstract: It is perhaps human nature to seek order in everything that surrounds us. With the number of individual viral particles in the biosphere considerably exceeding that of their hosts (33), the virosphere—or the viral universe, if you wish—shares this quest. In fact, the number of viruses is so high that the entire tree of cellular life, from its roots to the tips of its branches, seems to be immersed in the sea of viruses (5). The attempt to bring order to the virosphere is manifested in the work carried out by the International Committee on Taxonomy of Viruses (ICTV) (9), an official body consisting of numerous experts in the field of virology. The ICTV currently recognizes the hierarchical levels of order, family, subfamily, genus, and species. The dominant (but not exclusive) demarcation criterion employed to delineate viruses into different taxonomic levels is sequence comparison, the main advantage of which is the quantitative reflection of the divergence between taxa. Virus origin and evolution are issues that have never ceased to fascinate biologists and are currently highly debated (see recent studies, e.g., references 11-13, 16, 18-19, 21, 23, 27, and 34). Unfortunately, sequence comparisons do not reach far enough to recognize the relationships between viruses that diversified further back in time while leaving no detectable signal at the sequence level. However, new information, coming mainly from structural studies, might help us (i) to reveal deeper evolutionary connections between viruses that were not previously considered to be related and (ii) to establish biologically relevant higher levels of virus classification, thereby bringing additional biology to taxonomy.

Recombination among picornaviruses.

Abstract: Picornaviruses are small non-enveloped positive strand RNA viruses that can cause a wide range of clinical manifestations in humans and animals. Many of these viruses are highly diversified and globally prevalent. Natural recombination has been reported in most picornavirus genera and is a key genetic feature of these infectious agents. In several socially relevant picornavirus genera, such as enteroviruses, aphthoviruses, parechoviruses and cardioviruses, recombination, combined with dynamic global epidemiology, maintains virus species as a worldwide pool of genetic information. It can be suggested that on a short time scale recombination acts to promote virus diversity, and new recombinant forms of picornaviruses emerge frequently as 'snapshots' of this global pool. On a longer time scale, recombination maintains stability of a gene pool of a species by shuffling sequences and thus limiting divergence and speciation. This review covers existing evidence of recombination in most genera of the family Picornaviridae and possible implications for diagnostics, epidemiology and classification.

Arabidopsis thaliana as a model for the study of plant–virus co-evolution

Abstract: Understanding plant–virus coevolution requires wild systems in which there is no human manipulation of either host or virus To develop such a system, we analysed virus infection in six wild populations of Arabidopsis thaliana in Central Spain The incidence of five virus species with different life-styles was monitored during four years, and this was analysed in relation to the demography of the host populations Total virus incidence reached 70 per cent, which suggests a role of virus infection in the population structure and dynamics of the host, under the assumption of a host fitness cost caused by the infection Maximum incidence occurred at early growth stages, and co-infection with different viruses was frequent, two factors often resulting in increased virulence Experimental infections under controlled conditions with two isolates of the most prevalent viruses, cauliflower mosaic virus and cucumber mosaic virus, showed that there is genetic variation for virus accumulation, although this depended on the interaction between host and virus genotypes Comparison of QST-based genetic differentiations between both host populations with FST genetic differentiation based on putatively neutral markers suggests different selection dynamics for resistance against different virus species or genotypes Together, these results are compatible with a hypothesis of plant–virus coevolution

Human picobirnaviruses identified by molecular screening of diarrhea samples.

Abstract: The global threat of (re)emerging infectious viruses requires a more effective approach regarding virus surveillance and diagnostic assays, as current diagnostics are often virus species specific and not able to detect highly divergent or unknown viruses. A systematic exploration of viruses that infect humans is the key to effectively counter the potential public health threat caused by new and emerging infectious diseases. The human gut is a known reservoir of a wide variety of microorganisms, including viruses. In this study, Dutch clinical diarrhea samples for which no etiological agent could be identified by available cell culture, serological, or nucleic acid-based tests were gathered. Large-scale molecular RNA virus screening based on host nucleic acid depletion, sequence-independent amplification, and sequencing of partially purified viral RNA from a limited number of clinical diarrhea samples revealed four eukaryotic virus species. Among the detected viruses were a rhinovirus and a new picobirnavirus variant. In total, approximately 20% of clinical diarrhea samples contained human picobirnavirus sequences. The Dutch picobirnaviruses belonged to different phylogenetic clades and did not group with other picobirnaviruses according to year of isolation or host species. Interestingly, the average age of patients infected with picobirnavirus was significantly higher than that of uninfected patients. Our data show that sequence-independent amplification of partially purified viral RNA is an efficient procedure for identification of known and highly divergent new RNA viruses in clinical diarrhea samples.

Clarification and guidance on the proper usage of virus and virus species names.

Abstract: A pivotal step in the development of a consistent nomenclature for virus classification was the introduction of the virus species concept by the International Committee on Taxonomy of Viruses (ICTV) in 1991. Yet, almost two decades later, many virologists still are unable to differentiate between virus species and actual viruses. Here we attempt to explain the origin of this confusion, clarify the difference between taxa and physical entities, and suggest simple measures that could be implemented by ICTV Study Groups to make virus taxonomy and nomenclature more accessible to laboratory virologists.

Applying neural networks to classify influenza virus antigenic types and hosts

Abstract: Influenza viruses continue to evolve rapidly and are responsible for seasonal epidemics and occasional, but catastrophic, pandemics. We recently demonstrated the use of decision tree and support vector machine methods in classifying pandemic swine flu viral strains with high accuracy. Here, we applied the technique of artificial neural networks for the prediction of important influenza virus antigenic types (H1, H3, and H5) and hosts (Human, Avian, and Swine), which fulfills a critical need for a computational system for influenza surveillance. A comprehensive experiment on different k-mers and different binary encoding types showed classification based upon frequencies of k-mer nucleotide strings performed better than transformed binary data of nucleotides. It has been found for the first time that the accuracy of virus classification varies from host to host and from gene segment to gene segment. In particular, compared to avian and swine viruses, human influenza viruses can be classified with high accuracy, which indicates influenza virus strains might have become well adapted to their human host and hence less variation occurs in human viruses. In addition, the accuracy of host classification varies from genome segment to segment, achieving the highest values when using the HA and NA segments for human host classification. This research, along with our previous studies, shows machine learning techniques play an indispensable role in virus classification.

Borna Disease Virus

Abstract: The neurotropic virus, Borna disease virus (BDV), a member of a group of nonsegmented, negative strand ribonucleic acid (RNA) viruses (order Mononegavirales), infects warm-blooded animal species. Infection among mammals may be asymptomatic, produce neurobehavioral abnormalities, or result in fatal meningoencephalitis. It is unique among animal viruses in the order Mononegavirales in its nuclear localization of replication and transcription and distinctive in its capacity to establish persistent, non-cytolytic infection of the peripheral and central nervous systems. Natural infection, long described in horses and sheep, has more recently been recognized to extend to bird species in association with a related virus, avian bornavirus, as well as to divergent bornaviruses in reptiles, challenging established virus taxonomy. Nonhuman primates can be experimentally infected; however, natural infection of humans and nonhuman primates appears to be unusual. Decades-long controversy over a role for BDV infection in human neuropsychiatric illnesses has more recently waned. Nonetheless, the discovery that the genomes of humans as well as other vertebrate lineages contain remnants of BDV sequences has raised questions regarding potential evolutionary implications. Analysis of rodent models of infection has yielded insights into the mechanisms by which neurotropic agents and host immune and signaling pathway responses may impact upon developing or mature CNS circuitry to effect complex neurobehavioral disturbances.

Virology as biosystematics: towards understanding the viral infection biology.

Abstract: Large numbers of virus species exist in the realm of nature, and are now classified into distinct sub-groups based on their biochemical and biological characteristics (Knipe et al., 2007). Viruses are unique in their genomic composition, nucleocapsid/virion morphology, replication strategy, and/or target host. Even though viruses represent the smallest entity encoding a genetic program and are strictly dependent on hosts for their replication, they adapt themselves in a species-specific and dexterous manner to infect or persist in a wide variety of living things. In the course of interaction with hosts, viruses somehow find ecological niches to prosper their progenies. By studying how viruses interact with their respective hosts, we have learned much about life itself in the past hundred years. On the other hand, viral infections in host individuals may sometimes result in the diseases with visible symptoms. Although viruses are often coexistent with hosts, they can cause fatal infectious diseases in extraordinary cases. We also have taken many important lessons from the virally caused illness. The mission of research in virology today is to understand completely and systemically the biology and molecular biology of virus/host interaction. We virologists thus can contribute to the progress of life science and to the development of medical science. To achieve this aim, it is essentially necessary to integrate the concepts and methodologies of various scientific fields such as molecular/population genetics, biochemistry, genomics, epi-genomics, proteomics, transcriptomics, metabolomics, bioinformatics, and computational science into the biosystematics. Virology in nature is a multi-disciplinary affair. A typical and good example of this research flow is the history of studies on recently emerged human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) (Ho and Bieniasz, 2008). Highly specialized scientists of various fields have worked together and extensively to obtain fundamental knowledge on the HIV-1 virus and its interaction with humans, the only host with symptoms of disease, which led to the discovery of HIV-1 as the initial pathogen of human acquired immunodeficiency syndrome (AIDS) (Barre-Sinoussi et al., 1983). As a result of this multi-disciplinary approach to research, much is currently known about both basic as well as clinical aspects of HIV-1 and AIDS. The molecular basis for virus replication in target cells has been largely clarified, and drugs effective against the virus have been generated (Ho and Bieniasz, 2008). However, due to lack of appropriate animal model systems, studies aimed at elucidating viral events in vivo and, consequently, the discovery of more effective anti-viral strategies have been greatly hampered (Nomaguchi et al., 2008). Noteworthy, trials to develop anti-viral vaccines have been unsuccessful thereby underscoring the need for more suitable primate model research to answer basic questions about HIV-1 in vivo (Hayden, 2008; Watkins et al., 2008). In our laboratory, for instance, efforts have been made to generate a new class of HIV-1s that are tropic and pathogenic for macaque monkeys (Kamada et al., 2006; Igarashi et al., 2007; Nomaguchi et al., 2008). When successful, these viruses will provide the opportunity, not possible with currently available simian immunodeficiency virus (SIV) and SIV/HIV-1 chimeric viruses, to analyze the function of multiple HIV-1 genes in non-human primate species frequently used for experimental viral infections. In conclusion, virologists today must study viruses multilaterally. With the help of various specialists if necessary, they are required to analyze viruses and their interactions with hosts comprehensively and systemically. Only with such a multi-disciplinary experimental approach, will we be able to better understand how viruses work and in the position to educate and inform the lay public about the importance of our science to the well-being of mankind.

Molecular Characterization and Detection of African Oil Palm Ringspot Virus

Abstract: African oil palm ringspot virus (AOPRV) had been previously described as a fovea-like virus associated with a lethal disease of African oil palm (Elaeis guineensis) in South America The original report was based on partial sequence and a distant relationship between AOPRV and Apple stem pitting virus, Apricot latent virus and Grapevine rupestris stem pitting-associated virus, definitive species of the genus Foveapirus, family Flexiviridae We report the full sequence of the RNA genome of AOPRV, and demonstrate that this virus is more closely related to two unassigned virus species of the family Flexiviridae (Cherry green ring mottle virus and Cherry necrotic rusty mottle virus) than to any definitive species of the genus Foveavirus Thus, AOPRV should be considered as a new species of the Flexiviridae until the International Committee on Taxonomy of Viruses (ICTV) resolves the taxonomic status of the increasing number of unassigned species in this family The molecular characterization of AOPRV has provided a highly sensitive and reliable RT-PCR assay for the early detection of AOPRV in different genotypes of African, American (E oleifera) and hybrid oil palms

The Dictionary of Virology, 4th Edition

Abstract: Rapidly expanding technologies in the field of virology, identification of novel viral agents, and the 2005 report (8th edition) of the International Congress of Taxonomy of Viruses (ICTV) addressing reclassification of several viruses generated the 20% new material in Mahy’s 4th edition of The Dictionary of Virology. The previous edition of this book was published in 2001; the 2009 edition includes recent advancements, such as newly described viruses (e.g., severe acute respiratory syndrome (SARS) human coronavirus, human metapneumoviruses, bocaviruses, and Rabensburg virus), reclassification schemes of viruses (for instance, the unassigned Anellovirus genus), and descriptions of new technologies (e.g., microarray analyses and microRNAs) that have profoundly affected the field of virology. This comprehensive desk reference provides concise definitions of virologic terms; enables quick fact checking; and provides useful, often difficult to find, information—such as the origin of virus names, determination of ICTV-approved virus abbreviations, and locations and sources of viral isolations. An appendix of current ICTV-recognized virus families, subfamilies, genera, and type species is especially useful. However, this reference is limited to viruses infecting vertebrate hosts; thus, it excludes viruses of plants, bacteria, fungi, invertebrates (except for arboviruses that have dual replication cycles within invertebrates and vertebrate hosts) or viruses (the newly described virophages of mimiviruses). The increasing quantity of information about viruses of vertebrates ranging from fish to primates presented the author with considerable space difficulties. He compensated for this situation, however, by citing literature sources at the end of entries for readers seeking more information. Additionally, considerable cross-referencing enhances the utility of the book. On the basis of inclusion of new information in the field and my personal experience with previous editions of The Dictionary of Virology, I highly recommend this volume to students, virologists, microbiologists, and public health professionals interested in viruses of vertebrate hosts.

The Nature and Classification of Viruses

Abstract: 1 The Filterability of Viruses 2 The Nature of Viruses 3 Viruses should not be Confused with Virus Particles or Virions 4 Virus Classification and Nomenclature 5 The International Committee on Taxonomy of Viruses 6 The Species Issue in Virology 7 Virus Identification 8 The ICTV database (ICTVdB) 9 Names and Typography of Virus Species 10 A Possible Future Binomial Nomenclature for Virus Species Keywords: contagium vivum fluidum; International Committee on Taxonomy of viruses; virus species as polythetic classes; virus species as replicating lineages; ecological niche occupancy; quasi-species misnomer; virus species demarcation; ICTV database (ICTVdB)

A Short History of Research on Viruses

Abstract: 1 Introduction 2 The Foundations 3 Propagation of Viruses in the Laboratory 4 The Properties of Viruses 5 Classification of Viruses 6 Immunization and Antiviral Therapy 7 Conclusion Keywords: research on viruses; discovery of viruses; propagation in tissue culture; oncogenic viruses; average pore diameter (APD); centrifugation; tobacco mosaic virus (TMV); new variant CJD (nvCJD) syndrome; antiviral therapy

The Classification of Vertebrate Viruses

Abstract: 1 Introduction 2 Definition of Taxa 3 The Universal System of Virus Taxonomy 4 The Concept of the Virus Species 5 Phylogenetic Analysis and Taxonomy 6 Virus Evolution Keywords: classification of vertebrate viruses; virus genera; simplex virus genus; single-stranded DNA viruses; Circoviridae; Parvoviridae; double-stranded DNA viruses; family Iridoviridae